[2023-03-15 15:25:35,286] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:25:35,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:25:35,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference
[2023-03-15 15:25:36,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:25:36,401] [INFO] Task started: Prodigal
[2023-03-15 15:25:36,402] [INFO] Running command: cat /var/lib/cwl/stg2f4dccbd-a420-443d-a41e-07b5b0f58a87/OceanDNA-b29579.fa | prodigal -d OceanDNA-b29579/cds.fna -a OceanDNA-b29579/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:25:44,787] [INFO] Task succeeded: Prodigal
[2023-03-15 15:25:44,787] [INFO] Task started: HMMsearch
[2023-03-15 15:25:44,787] [INFO] Running command: hmmsearch --tblout OceanDNA-b29579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/reference_markers.hmm OceanDNA-b29579/protein.faa > /dev/null
[2023-03-15 15:25:44,947] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:25:44,948] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f4dccbd-a420-443d-a41e-07b5b0f58a87/OceanDNA-b29579.fa]
[2023-03-15 15:25:45,005] [INFO] Query marker FASTA was written to OceanDNA-b29579/markers.fasta
[2023-03-15 15:25:45,007] [INFO] Task started: Blastn
[2023-03-15 15:25:45,007] [INFO] Running command: blastn -query OceanDNA-b29579/markers.fasta -db /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/reference_markers.fasta -out OceanDNA-b29579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:25:45,637] [INFO] Task succeeded: Blastn
[2023-03-15 15:25:45,651] [INFO] Selected 12 target genomes.
[2023-03-15 15:25:45,652] [INFO] Target genome list was writen to OceanDNA-b29579/target_genomes.txt
[2023-03-15 15:25:45,659] [INFO] Task started: fastANI
[2023-03-15 15:25:45,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f4dccbd-a420-443d-a41e-07b5b0f58a87/OceanDNA-b29579.fa --refList OceanDNA-b29579/target_genomes.txt --output OceanDNA-b29579/fastani_result.tsv --threads 1
[2023-03-15 15:25:52,662] [INFO] Task succeeded: fastANI
[2023-03-15 15:25:52,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:25:52,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:25:52,720] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:25:52,720] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:25:52,720] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	79.4846	269	417	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	78.8183	248	417	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	76.1985	69	417	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	75.9996	66	417	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	75.9751	67	417	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:25:52,723] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29579/tc_result.tsv
[2023-03-15 15:25:52,725] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:25:52,725] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:25:52,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/checkm_data
[2023-03-15 15:25:52,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:25:52,736] [INFO] Task started: CheckM
[2023-03-15 15:25:52,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29579/checkm_input OceanDNA-b29579/checkm_result
[2023-03-15 15:26:21,101] [INFO] Task succeeded: CheckM
[2023-03-15 15:26:21,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:26:21,201] [INFO] ===== Completeness check finished =====
[2023-03-15 15:26:21,201] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:26:21,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29579/markers.fasta)
[2023-03-15 15:26:21,202] [INFO] Task started: Blastn
[2023-03-15 15:26:21,202] [INFO] Running command: blastn -query OceanDNA-b29579/markers.fasta -db /var/lib/cwl/stg82445eb1-a50f-4127-9771-cff22e8bdb92/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:26:22,363] [INFO] Task succeeded: Blastn
[2023-03-15 15:26:22,371] [INFO] Selected 16 target genomes.
[2023-03-15 15:26:22,371] [INFO] Target genome list was writen to OceanDNA-b29579/target_genomes_gtdb.txt
[2023-03-15 15:26:22,387] [INFO] Task started: fastANI
[2023-03-15 15:26:22,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f4dccbd-a420-443d-a41e-07b5b0f58a87/OceanDNA-b29579.fa --refList OceanDNA-b29579/target_genomes_gtdb.txt --output OceanDNA-b29579/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:26:30,275] [INFO] Task succeeded: fastANI
[2023-03-15 15:26:30,280] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:26:30,280] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000155675.2	s__Octadecabacter antarcticus	79.4846	269	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.8466	240	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	78.8183	248	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCA_018608045.1	s__Octadecabacter sp018608045	76.714	70	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_018861045.1	s__Octadecabacter sp018861045	76.4435	51	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	76.1985	69	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	75.9996	66	417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:26:30,284] [INFO] GTDB search result was written to OceanDNA-b29579/result_gtdb.tsv
[2023-03-15 15:26:30,286] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:26:30,289] [INFO] DFAST_QC result json was written to OceanDNA-b29579/dqc_result.json
[2023-03-15 15:26:30,290] [INFO] DFAST_QC completed!
[2023-03-15 15:26:30,290] [INFO] Total running time: 0h0m55s